[Camino-users] problem with mbalign.

[Darren Gitelman]

Hi

I am trying to use camino to analyze my DTI data.

I am first doing eddy current correction.

This is my command line:

[drg at zonda camino]$ mbalign -datatype float -schemefile
36dwi_b1000_bvector.scheme -components 36 -datadims 260 260 65 -voxeldims
.73846 .73846 2.0 -sigma 14 -inputfile dti001_ser7.Bfloat -bgmask
dti001_mask.nii -eddy -outputfile dti001_ser7_eddy.Bfloat -slicecheck
/data/zonda1/pddti/dti001/camino/slicecheck/dti001_slicecheck -bgthresh 20

This gives me some initial output:

:-) I have everything I need!
36 components inside inputfile.
No temp directory specified. Trying to use /tmp/dti001_ser7_15.11.11_181736.
Successfully created /tmp/dti001_ser7_15.11.11_181736.
Linux system detected.
Disk space temporarily used during calculation is about 5694624000. Make
sure space is available!
Fitting Tensors...
mask input

After this I get a lot of output that looks like the following. I get this
output whether or not I specify a bgthresh and at a variety of sigma
values. Is this to be expected or do I need to fix something?

Nov 15, 2011 6:17:42 PM imaging.DW_Scheme normalizeData
WARNING: Can't use normalization constant 0.0
Nov 15, 2011 6:17:42 PM inverters.RestoreDT_Inversion invert
INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj -
2  Fitting failed.  Outputting best DT found, which may be affected by
outliers.
Nov 15, 2011 6:17:43 PM imaging.DW_Scheme normalizeData
WARNING: Can't use normalization constant 0.0
Nov 15, 2011 6:17:43 PM inverters.RestoreDT_Inversion invert
INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj -
2  Fitting failed.  Outputting best DT found, which may be affected by
outliers.
Nov 15, 2011 6:17:45 PM imaging.DW_Scheme normalizeData
WARNING: Can't use normalization constant 0.0
Nov 15, 2011 6:17:45 PM inverters.RestoreDT_Inversion invert
INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj -
2  Fitting failed.  Outputting best DT found, which may be affected by
outliers.
Nov 15, 2011 6:17:47 PM imaging.DW_Scheme normalizeData
WARNING: Can't use normalization constant 0.0
Nov 15, 2011 6:17:47 PM inverters.RestoreDT_Inversion invert
INFO: optimizers.MarquardtMinimiserException: Singular Matrix in gaussj -
2  Fitting failed.  Outputting best DT found, which may be affected by
outliers.
Nov 15, 2011 6:17:57 PM inverters.RestoreDT_Inversion invert
INFO: Maximum iterations reached without convergence. Final tensor:
        1.2312659747573168E-9 -1.0053586166159994E-10
-1.4422426735710772E-11
-1.0053586166159994E-10 1.0873050187771824E-9 2.6988536554535517E-11
-1.4422426735710772E-11 2.6988536554535517E-11 9.300247616640151E-10

-- 
Darren
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